Improve version of the TOP software package for automatic
comparison of 3-d protein structures
The TOP program for automatic comparisons of protein structures has been
recently improved. The new version for unix computers can be obtained
via FTP. The new version of Web server has been also installed. Please
see http://gamma.mbb.ki.se/~guoguang/webtop/wwwtop.html
The most significant improvement is in seraching similar structures in
database. The users of old version complained about the program outputs
too much infomration (noise) which is diffult to get the point. The new
version gives parameters of "Structure Diveristy" and "Topological
Diversity" which rank the similarity between homologous structures. It
is much easier for users to find the their most similar structures in
the search and igored the noise.
The new version is able to find sequence permutations in the comparisons
This will help to find homologous structures which is missed the other
software with similar functions.
Some part of the document mightbe still confusing. I need feed back from
users to fix it. It is also welcome to complain about any problems of
Web server and unix computers.
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Guoguang Lu, PhD, Research Scientist
Division of Molecular Structural Biology
Department of Medical Biochemistry and Biophysics
Doktorsringen 9A1
Karolinska Institute
17177 Stockholm
Sweden
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Phone: (int+46)-8-728 7651(o) Email: guoguang at alfa.mbb.ki.se
Fax: (int+46)-8-327626 Homepage: http://gamma.mbb.ki.se/~guoguang
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